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A plugin that enables annotations provided by Allen Institute for Cell Science

Project description


License BSD-3 PyPI Python Version tests codecov napari hub

A plugin to use with napari to annotate images and export .csv data

The Allen Cell Image Annotator plugin for napari provides an intuitive graphical user interface to create, add, and export custom image annotations on large data sets. The Allen Cell Image Annotator is a Python-based open source toolkit developed at the Allen Institute for Cell Science. This toolkit allows users to easily upload, shuffle, and hide images. Users can create annotations (text, checkbox, drop-down, and spinbox) which are rendered into a custom user interface and can be applied to the uploaded images. Annotation data is exported into a .csv file.

  • Supports the following image types:
    • OME-TIFF
    • TIFF
    • CZI
    • PNG
    • JPEG

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.


You can install napari-allencell-annotator via pip:

pip install napari-allencell-annotator

To install latest development version :

pip install git+

Quick Start

In the current version, there are two parts in the plugin: Image Uploader and Annotator. The Annotator allows users to create new or upload existing annotations and apply those annotations on the image set they create in the Image Uploader section of the plugin.

To install latest development version :

pip install git+


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.


Distributed under the terms of the BSD-3 license, "napari-allencell-annotator" is free and open source software


If you encounter any problems, please file an issue along with a detailed description.

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napari-allencell-annotator-0.0.3.tar.gz (23.9 kB view hashes)

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